I hope the battery has enough juice left in it to activate the computer which controls the engine and immobiliser functions. Also it is possible that any voltage surge may harm the bikes electronics though I imagine BWM have engineered it to be a little more robust than that.
If I were you, I would go out and buy an Optimate or similar immediately and connect it to the battery, if it has only recently discharged it should fully recover it within a few hours before any plate sulphation takes place and kills it permanently. Once recovered, you can start the bike again safely without any voltage spikes frying anything then keep it optimated when not riding to maintain the battery. They are about £35 and worth every penny ( a new battery is twice that amount). The heated grip controller on my Yamaha shorted and flattened the battery, but my optimate recovered the battery once I disconnected the grips and it still performs fine now. A full charge/discharge/charge cycle is beneficial for battery health but leaving one fully discharged for any length of time does serious harm to the battery.
My R1200GS does not discharge the battery when left standing, so I guess long-term you need a dealer to look at the bike and find out why, then fix it under warranty.